I've had a look again this morning, and even tried creating a new style to see if there was any unintentional styles errors... but so far it look just the same.
It might be worth investigating whether storing the style as files might help (in the vBOptions), but I doubt it will fix it. Since disabling the hooks leaves the issue as it is, that would suggest that there is a problem outside of DFT.
It might be worth posting on the vB site to see if they can offer any suggestions. Maybe before that upload all your vB files again in case there is an edit in the files that's causing the issues.
I'll mark this thread as not a bug, but feel free to let me know how you get on,